Antigen Tracking Figures
Ryan Sheridan
2023-11-28
Cell type annotations
Figure 1
Antigen persists in discrete cell subsets within the lymph node
- Experiment 1 is shown for the LEC 21 and 42 day timepoints. Experiment 2 data include very few LECs for the 21 day timepoint.
- Experiment 2 is shown for the DC 21 and 42 day timepoints. Experiment 1 data are lower quality.
- Subsets are only shown if there are >= 5 cells for each timepoint
- CHECK AG ACORES FOR NEUTROPHILS
Extended figures
Ag-score is shown for all LEC subsets for each experiment
Ag-score is shown for all DC subsets for each experiment
Figure 2
Figure 3
- p-values were calculated using a t test with bonferroni correction
- ADD AG MODULE BOXPLOTS
Extended figures
Day 21 Ag-score is shown for all subsets for each experiment
Day 42 Ag-score is shown for all subsets for each experiment
Session info
## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
## [9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
##
## time zone: America/Denver
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 tools grid stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] ggtree_3.8.2 GOSemSim_2.26.1 org.Mm.eg.db_3.17.0
## [4] AnnotationDbi_1.62.2 IRanges_2.34.1 S4Vectors_0.38.2
## [7] Biobase_2.60.0 BiocGenerics_0.46.0 msigdbr_7.5.1
## [10] enrichplot_1.20.3 clusterProfiler_4.8.3 caret_6.0-94
## [13] lattice_0.21-8 furrr_0.3.1 future_1.33.0
## [16] ranger_0.15.1 rsample_1.2.0 harmony_1.1.0
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## [25] vroom_1.6.4 M3Drop_1.26.0 numDeriv_2016.8-1.1
## [28] djvdj_0.1.0 gtools_3.9.4 clustifyrdata_1.1.0
## [31] here_1.0.1 presto_1.0.0 data.table_1.14.8
## [34] Rcpp_1.0.11 devtools_2.4.5 usethis_2.2.2
## [37] ComplexHeatmap_2.16.0 patchwork_1.1.3 scales_1.2.1
## [40] boot_1.3-28.1 clustifyr_1.12.0 mixtools_2.0.0
## [43] broom_1.0.5 colorblindr_0.1.0 colorspace_2.1-0
## [46] xlsx_0.6.5 RColorBrewer_1.1-3 ggrepel_0.9.3
## [49] cowplot_1.1.1 knitr_1.44 gprofiler2_0.2.2
## [52] SeuratObject_4.1.4 Seurat_4.4.0 ggforce_0.4.1
## [55] ggbeeswarm_0.7.2 lubridate_1.9.3 forcats_1.0.0
## [58] stringr_1.5.0 dplyr_1.1.3 purrr_1.0.2
## [61] readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
## [64] ggplot2_3.4.3 tidyverse_2.0.0
##
## loaded via a namespace (and not attached):
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## [3] plotly_4.10.2 Formula_1.2-5
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## [11] blob_1.2.4 urlchecker_1.0.1
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